OLIGONUCLEOTIDES CONTAINING G-CENTER-DOT-A PAIRS - EFFECT OF FLANKING SEQUENCES ON STRUCTURE AND STABILITY

Sixteen oligodeoxyribonucleotides, 5'd(GXGAYC)3', X and Y = G, A, C, or have been synthesized and studied by UV melting and H-1 and P-31 NMR methods. By varying X and Y, the sixteen resulting oligonucleotides can theoretically form 10 duplexes with all possible Watson-Crick base pairs flanking the center two G . A base pairs. Two-dimensional H-1 NMR data on 5'd(GCGAGC)3' revealed that the center bases G and A pair through G amino hydrogen bonding and that the two consecutive G . A pairs form excellent purine-purine stacks. The concurrent appearance of one or more upfield-shifted imino proton peaks (similar to 10.5 ppm) and both upfield- and downfield- shifted P-31 signals (similar to-2 and similar to-5.1 ppm) was a unique characteristic in imino H-1 and P-31 NMR spectra and was used as a conformational probe for this type of G . A pairs. Using this probe, seven out of 10 duplexes of 5'GXGAYC3' were found to adopt the G . A base pairing with G amino proton bonding and G to G and A to A base stacking. Three were in the group comprising 5'pyrimidine-GA-purine3', and four were in the group comprising 5'purine-GA-purine3'/5' pyrimidine-GA-pyrimidine3'. The G A pairs in 5'purine-GA-pyrimidine3' adopted a totally different conformation. Thermodynamic analysis indicated that duplexes in the 5'pyrimidine-GA-purine3' group were more stable than the duplexes in the 5'purine-GA-pyrimidine3' group. Overall, G . C base pairs were preferred as neighbors to this type of G . A pairs.